MolNFT v1 · #89244 · protein
Crystal structure of a ribonucleotide reductase M2 B (RNRR2) from homo sapiens at 2.20 a resolution
4DJN · Ribonucleoside-diphosphate reductase subunit M2 B: “Crystal structure of a ribonucleotide reductase M2 B (RNRR2) from homo sapiens at 2.20 a resolution”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.84). MolNFT…
- PDB
- 4DJN
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase subunit M2 B
- EC
- 1.17.4.1
- UniProt
- Q7LG56
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase subunit M2 B (EC 1.17.4.1) | protein | 287 | 74% helix, 0% strand | Q7LG56 |
| B | Ribonucleoside-diphosphate reductase subunit M2 B (EC 1.17.4.1) | protein | 287 | 73% helix, 0% strand | Q7LG56 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.84 | 0.90 | 54 | empty |
| 2 | 164 | 0.52 | 0.79 | 24 | empty |
| 3 | 172 | 0.50 | 0.77 | 24 | empty |
| 4 | 111 | 0.36 | 0.73 | 21 | EDO |
| 5 | 73 | 0.34 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1707 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4DJN · Crystal structure of a ribonucleotide reductase M2 B (RNRR2) from Homo sapiens at 2.20 A… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7LG56 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase subunit M2 B… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q7LG56
- Elsewhere: RCSB PDB 4DJN · PDBe 4DJN · UniProt Q7LG56
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